The three federal agencies that support the vast majority of academic research would receive no more money in 2011 than in 2010 under a spending bill that narrowly passed the House of Representatives last night. Although the Senate is working on a different version that would provide small increases for those agencies, the House vote is a clear signal that Congress has entered a new era of fiscal austerity.

Despite the opposition of 35 Democrats, the House leadership prevailed on a 212 to 206 vote that would hold overall discretionary spending to $1.09 trillion. That figure matches 2010 spending levels and is $46 billion below what President Barack Obama had requested for 2011.

The House bill contains a few winners for the research community, including space science at NASA, the new Advanced Research Projects Agency-Energy (ARPA-E) at the Department of Energy, and competitive agriculture research. But that's a meager harvest for those hoping for the generous increases—7% for the National Science Foundation (NSF), 3.2% for the National Institutes of Health (NIH), and 4.4% for the Department of Energy's Office of Science—that Obama had sought in a budget he submitted in February. Of course, that was before last month's election, in which Republicans reclaimed the House, based in large part on a promise to shrink government spending.

"Yes, we must deal with long-term budget deficits," said the chair of the House Appropriations Committee, Representative David Obey (D-WI), in an angry statement on the House floor before the vote. "But if this country is to grow for everybody, we also need to confront our investment deficits in jobs, in education, in infrastructure, and science and technology."

Obey, who is retiring this month after 42 years in the House, said that "there are at least 50 decisions in this bill that I am flatly opposed to. There are many arguments in this bill that I have lost. But the fact is, sooner or later, if you're going to be responsible, you have to set aside your first preferences and simply do what is necessary in order to keep the government open."

Some segments of the research community would get their preferences under the House spending bill. For example, it matches the president's request for a 1.5% increase for NASA, to $19 billion, including a 12% increase, to $5 billion, for the space science program. Legislators had already worked out a deal with the White House on the future of the manned space program, and they included funding for an additional shuttle flight in 2011. They even added $35 million to the $20 million increase that the president requested for NASA's education programs, boosting them by a whopping 30% to $180 million.

The House bill granted the president's request for $300 million for ARPA-E, specifying that DOE may pay for it by using funds from the $4.9 billion Office of Science and its Energy Efficiency and Renewable Energy program. The lawmakers reiterated previous language that allows ARPA-E to pay its employees above the standard pay scale dictated by civil service laws.

"It's a great sign that [ARPA-E] has the $300 million," said former Senate energy aide Timothy Valentine, now a researcher at DOE's Oak Ridge National Laboratory. But he fears the agency could suffer with the retirement of Representative Bart Gordon (D-TN), chair of the House science committee. "I think that's all going to change. ... With Gordon gone, who's the big champion for it?" He added: "I hope I'm completely wrong."

The bill also provides a 2.5% increase in the competitive grants program within the revamped National Institute of Food and Agriculture at the Department of Agriculture, growing the $262 million program to $269 million. The president had requested a 63% boost.

Agencies with flat funding may still be able to shift some money around to emphasize agency priorities. But they must stay within the overall ceiling imposed by Congress. "I expect that we will be allowed some flexibility below the appropriated account levels," says Anthony Gibson, head of legislative affairs for NSF. "But the funding levels for those accounts will be set based on the FY '10 appropriated level and are immutable."

Although the continuing resolution holds NIH at the $31 billion it had in 2010, it allows the agency to spend up to $25 million on the Cures Acceleration Network, a drug-development program created by the health reform law enacted earlier this year. The agency would fare better in the draft Senate omnibus bill, which is said to contain a $750 million increase (2.4%) for NIH. Although short of the $1 billion that the president requested and House and Senate spending panels approved earlier this year, it would be enough to provide "a modest amount of relief," said NIH Director Francis Collins at an advisory board meeting this morning. "Certainly from NIH's perspective, we would hope that would happen," said Collins.

But the prospects that the Senate will muster the 60 votes needed to pass the omnibus are "very remote," says David Moore, head of governmental relations for the Association of American Medical Colleges in Washington, D.C. And if NIH stays at the 2010 level, Moore says, "There's no question we're going to see continued declines in success rates," or the percentage of submitted applications that are funded, as NIH exhausts the $10 billion in stimulus funding it received last year.

Flat funding for 2011 and beyond would be equally devastating for the physical sciences, says American Physical Society lobbyist Michael Lubell, who argues that, more than ever, scientists need to demonstrate the value of basic research. "The community is not hearing the message," says Lubell. "The message is that if momentum builds on constraining spending, science is going to be hit, unless we can show that the investments are worth it."